<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.17"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>SPHinXsys: SPHINXsys/src/shared/particle_dynamics/diffusion_reaction_dynamics/particle_dynamics_diffusion_reaction.h Source File</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  <td id="projectlogo"><img alt="Logo" src="logo.png"/></td>
  <td id="projectalign" style="padding-left: 0.5em;">
   <div id="projectname">SPHinXsys
   &#160;<span id="projectnumber">alpha version</span>
   </div>
  </td>
 </tr>
 </tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.17 -->
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
var searchBox = new SearchBox("searchBox", "search",false,'Search');
/* @license-end */
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
/* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&amp;dn=gpl-2.0.txt GPL-v2 */
$(function() {
  initMenu('',true,false,'search.php','Search');
  $(document).ready(function() { init_search(); });
});
/* @license-end */</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>

<div id="nav-path" class="navpath">
  <ul>
<li class="navelem"><a class="el" href="dir_3dc1dabd28ba78e072d14d3fcfc90454.html">SPHINXsys</a></li><li class="navelem"><a class="el" href="dir_48ea983704c43b6d88c1fa3f4d09e369.html">src</a></li><li class="navelem"><a class="el" href="dir_0a0d9ef1793521534f0094f317758287.html">shared</a></li><li class="navelem"><a class="el" href="dir_05f659066ce4fa1dc9c19bd298f55a53.html">particle_dynamics</a></li><li class="navelem"><a class="el" href="dir_4df800dd465e306f983e2b011c0f5cce.html">diffusion_reaction_dynamics</a></li>  </ul>
</div>
</div><!-- top -->
<div class="header">
  <div class="headertitle">
<div class="title">particle_dynamics_diffusion_reaction.h</div>  </div>
</div><!--header-->
<div class="contents">
<a href="particle__dynamics__diffusion__reaction_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/* -------------------------------------------------------------------------*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">*                               SPHinXsys                                   *</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">* --------------------------------------------------------------------------*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* SPHinXsys (pronunciation: s&#39;finksis) is an acronym from Smoothed Particle *</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* Hydrodynamics for industrial compleX systems. It provides C++ APIs for    *</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* physical accurate simulation and aims to model coupled industrial dynamic *</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* systems including fluid, solid, multi-body dynamics and beyond with SPH   *</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* (smoothed particle hydrodynamics), a meshless computational method using  *</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">* particle discretization.                                                  *</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">* SPHinXsys is partially funded by German Research Foundation               *</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">* (Deutsche Forschungsgemeinschaft) DFG HU1527/6-1, HU1527/10-1             *</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">* and HU1527/12-1.                                                          *</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">* Portions copyright (c) 2017-2020 Technical University of Munich and       *</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">* the authors&#39; affiliations.                                                *</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">* Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may   *</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">* not use this file except in compliance with the License. You may obtain a *</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">* copy of the License at http://www.apache.org/licenses/LICENSE-2.0.        *</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">* --------------------------------------------------------------------------*/</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160; </div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="preprocessor">#include &quot;all_particle_dynamics.h&quot;</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="diffusion__reaction__particles_8h.html">diffusion_reaction_particles.h</a>&quot;</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="preprocessor">#include &quot;diffusion_reaction.h&quot;</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160; </div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160; </div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;{</div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;    <span class="keyword">using</span>  DiffusionReactionSimpleData = DataDelegateSimple&lt;BodyType,</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;,</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;        DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;&gt;;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160; </div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    <span class="keyword">using</span> DiffusionReactionInnerData = DataDelegateInner&lt;BodyType,</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;,</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;        DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;&gt;;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160; </div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span>BaseParticlesType, <span class="keyword">class </span>BaseMaterialType,</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;        <span class="keyword">class </span>ContactBodyType, <span class="keyword">class </span>ContactBaseParticlesType, <span class="keyword">class </span>ContactBaseMaterialType&gt;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;    <span class="keyword">using</span> DiffusionReactionContactData = DataDelegateContact&lt;BodyType,</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;,</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;        DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;,</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;        ContactBodyType, DiffusionReactionParticles&lt;ContactBaseParticlesType, ContactBaseMaterialType&gt;,</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;        ContactBaseMaterialType, DataDelegateEmptyBase&gt;;</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160; </div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">   61</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">DiffusionReactionInitialCondition</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;        <span class="keyword">public</span>  <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    {</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">DiffusionReactionInitialCondition</a>(BodyType* diffusion_body);</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">DiffusionReactionInitialCondition</a>() {};</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;        StdLargeVec&lt;Vecd&gt;&amp; pos_n_;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    };</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160; </div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">   78</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a> :</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;        <span class="keyword">public</span>  <a class="code" href="class_s_p_h_1_1_particle_dynamics.html">ParticleDynamics</a>&lt;Real&gt;,</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    {</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a>(BodyType* body);</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a>() {};</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160; </div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">   86</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">exec</a>(Real dt = 0.0)<span class="keyword"> override </span>{ <span class="keywordflow">return</span> diff_time_step_; };</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;        <span class="keyword">virtual</span> Real parallel_exec(Real dt = 0.0)<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">exec</a>(dt); };</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;        <a class="code" href="class_real.html">Real</a> diff_time_step_;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    };</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160; </div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_inner.html">   97</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_inner.html">RelaxationOfAllDiffussionSpeciesInner</a> :</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_interaction_dynamics_with_update.html">InteractionDynamicsWithUpdate</a>,</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_inner.html">DiffusionReactionInnerData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    {</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;        StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; diffusion_dt_;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;        StdLargeVec&lt;Real&gt;&amp; Vol_;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        <span class="keywordtype">void</span> initializeDiffusionChangeRate(<span class="keywordtype">size_t</span> particle_i);</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        <span class="keywordtype">void</span> getDiffusionChangeRate(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd&amp; e_ij, Real surface_area_ij);</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> updateSpeciesDiffusion(<span class="keywordtype">size_t</span> particle_i, Real dt);</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Interaction(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;        <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_inner.html">RelaxationOfAllDiffussionSpeciesInner</a>(<a class="code" href="class_s_p_h_1_1_base_inner_body_relation.html">BaseInnerBodyRelation</a>* body_inner_relation);</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_inner.html">RelaxationOfAllDiffussionSpeciesInner</a>() {};</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    };</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160; </div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span>BaseParticlesType, <span class="keyword">class </span>BaseMaterialType,</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        <span class="keyword">class </span>ContactBodyType, <span class="keyword">class </span>ContactBaseParticlesType, <span class="keyword">class </span>ContactBaseMaterialType&gt;</div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_complex.html">  123</a></span>&#160;        <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_complex.html">RelaxationOfAllDiffussionSpeciesComplex</a> :</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_inner.html">RelaxationOfAllDiffussionSpeciesInner</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;,</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_contact.html">DiffusionReactionContactData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType,</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;        ContactBodyType, ContactBaseParticlesType, ContactBaseMaterialType&gt;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    {</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;        StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; diffusion_dt_;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;*&gt; contact_Vol_;</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;        StdVec&lt;StdVec&lt; StdLargeVec&lt;Real&gt;&gt;*&gt; contact_species_n_;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;        <span class="keywordtype">void</span> getDiffusionChangeRateContact(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd&amp; e_ij, </div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;            Real surface_area_ij, StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_k);</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Interaction(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;        <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_complex.html">RelaxationOfAllDiffussionSpeciesComplex</a>(<a class="code" href="class_s_p_h_1_1_complex_body_relation.html">ComplexBodyRelation</a>* body_complex_relation);</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_complex.html">RelaxationOfAllDiffussionSpeciesComplex</a>() {};</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;    };</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160; </div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_runge_kutta_initialization.html">  147</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_runge_kutta_initialization.html">RungeKuttaInitialization</a> :</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;    {</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;        StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_, &amp; species_s_;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160; </div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;        <span class="keywordtype">void</span> initializeIntermediateValue(<span class="keywordtype">size_t</span> particle_i);</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;        <a class="code" href="class_s_p_h_1_1_runge_kutta_initialization.html">RungeKuttaInitialization</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body.html">SPHBody</a>* body, StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_s);</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_runge_kutta_initialization.html">RungeKuttaInitialization</a>() {};</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    };</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160; </div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> RungeKutta2Stages1stStageType, <span class="keyword">class</span> BodyRelationType&gt;</div>
<div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_runge_kutta2_stages2nd_stage.html">  166</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_runge_kutta2_stages2nd_stage.html">RungeKutta2Stages2ndStage</a> : <span class="keyword">public</span> RungeKutta2Stages1stStageType</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;    {</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;        StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; diffusion_dt_;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_s_;</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> updateSpeciesDiffusion(<span class="keywordtype">size_t</span> particle_i, Real dt) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;        <a class="code" href="class_s_p_h_1_1_runge_kutta2_stages2nd_stage.html">RungeKutta2Stages2ndStage</a>(BodyRelationType* body_relation, StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_s);</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_runge_kutta2_stages2nd_stage.html">RungeKutta2Stages2ndStage</a>() {};</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;    };</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160; </div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span>BaseParticlesType, <span class="keyword">class </span>BaseMaterialType,</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;        <span class="keyword">class </span>RungeKutta2Stages1stStageType, <span class="keyword">class </span>BodyRelationType&gt;</div>
<div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">  186</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics.html">ParticleDynamics</a>&lt;void&gt;,</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;    {</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;        StdVec&lt;BaseDiffusion*&gt; species_diffusion_;</div>
<div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#a7e1a1c79e4b69348aea7e9644fe1de57">  192</a></span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#a7e1a1c79e4b69348aea7e9644fe1de57">species_s_</a>;</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160; </div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;        <a class="code" href="class_s_p_h_1_1_runge_kutta_initialization.html">RungeKuttaInitialization&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a> runge_kutta_initialization_;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;        RungeKutta2Stages1stStageType runge_kutta_1st_stage_;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;        <a class="code" href="class_s_p_h_1_1_runge_kutta2_stages2nd_stage.html">RungeKutta2Stages2ndStage&lt;RungeKutta2Stages1stStageType, BodyRelationType&gt;</a> runge_kutta_2nd_stage_;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;        <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2</a>(BodyRelationType* body_relation);</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2</a>() {};</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160; </div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#aa22ce7bc1d540b7e691544bd8cf556c0">exec</a>(Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> parallel_exec(Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    };</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160; </div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160; </div>
<div class="line"><a name="l00206"></a><span class="lineno"><a class="line" href="struct_s_p_h_1_1_update_a_reaction_species.html">  206</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="struct_s_p_h_1_1_update_a_reaction_species.html">UpdateAReactionSpecies</a></div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;    {</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;        Real operator () (Real input, Real production_rate, Real loss_rate, Real dt)<span class="keyword"> const </span></div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;<span class="keyword">        </span>{ </div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;            <span class="keywordflow">return</span> input * exp(-loss_rate * dt) + production_rate * (1.0 - exp(-loss_rate * dt)) / (loss_rate + TinyReal);</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;        };</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;    };</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160; </div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00219"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">  219</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">RelaxationOfAllReactionsForward</a> :</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;    {</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* species_reaction_;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;        <a class="code" href="struct_s_p_h_1_1_update_a_reaction_species.html">UpdateAReactionSpecies</a> updateAReactionSpecies;</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;        <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">RelaxationOfAllReactionsForward</a>(BodyType* body);</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">RelaxationOfAllReactionsForward</a>() {};</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;    };</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160; </div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">  238</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">RelaxationOfAllReactionsBackward</a> :</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;    {</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a>* species_reaction_;</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;        <a class="code" href="struct_s_p_h_1_1_update_a_reaction_species.html">UpdateAReactionSpecies</a> updateAReactionSpecies;</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;        <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">RelaxationOfAllReactionsBackward</a>(BodyType* body);</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">RelaxationOfAllReactionsBackward</a>() {};</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;    };</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160; </div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BodyPartByParticleType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00257"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">  257</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">ConstrainDiffusionBodyRegion</a> :</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_part_simple_dynamics_by_particle.html">PartSimpleDynamicsByParticle</a>,</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;    {</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;        <a class="code" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">ConstrainDiffusionBodyRegion</a>(BodyType* body, BodyPartByParticleType* body_part) :</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;            <a class="code" href="class_s_p_h_1_1_part_simple_dynamics_by_particle.html">PartSimpleDynamicsByParticle</a>(body, body_part),</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;            <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body),</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;            pos_n_(this-&gt;particles_-&gt;pos_n_), species_n_(this-&gt;particles_-&gt;species_n_) {};</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">ConstrainDiffusionBodyRegion</a>() {};</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;        StdLargeVec&lt;Vecd&gt;&amp; pos_n_;</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;    };</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160; </div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div>
<div class="line"><a name="l00278"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_based_mapping.html">  278</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a> :</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;        <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;    {</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a>(BodyType* body) :</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;            <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>(body),</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;            <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body),</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;            pos_n_(this-&gt;particles_-&gt;pos_n_), species_n_(this-&gt;particles_-&gt;species_n_) {};</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a>() {};</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;        StdLargeVec&lt;Vecd&gt;&amp; pos_n_;</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt;&amp; species_n_;</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;    };</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;}</div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="aclass_s_p_h_1_1_data_delegate_contact_html"><div class="ttname"><a href="class_s_p_h_1_1_data_delegate_contact.html">SPH::DataDelegateContact</a></div><div class="ttdoc">prepare data for contact particle dynamics</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:213</div></div>
<div class="ttc" id="adiffusion__reaction__particles_8h_html"><div class="ttname"><a href="diffusion__reaction__particles_8h.html">diffusion_reaction_particles.h</a></div><div class="ttdoc">This is the derived class of diffusion reaction particles.</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html_aa22ce7bc1d540b7e691544bd8cf556c0"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#aa22ce7bc1d540b7e691544bd8cf556c0">SPH::RelaxationOfAllDiffusionSpeciesRK2::exec</a></div><div class="ttdeci">virtual void exec(Real dt=0.0) override</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.hpp:244</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_runge_kutta2_stages2nd_stage_html"><div class="ttname"><a href="class_s_p_h_1_1_runge_kutta2_stages2nd_stage.html">SPH::RungeKutta2Stages2ndStage</a></div><div class="ttdoc">the second stage of the second runge-kutta scheme</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:166</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_complex_body_relation_html"><div class="ttname"><a href="class_s_p_h_1_1_complex_body_relation.html">SPH::ComplexBodyRelation</a></div><div class="ttdoc">The relation combined an inner and a contactbody relation. The interaction is in a inner-boundary-con...</div><div class="ttdef"><b>Definition:</b> body_relation.h:224</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_relaxation_of_all_diffussion_species_complex_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_complex.html">SPH::RelaxationOfAllDiffussionSpeciesComplex</a></div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:123</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">SPH::RelaxationOfAllDiffusionSpeciesRK2</a></div><div class="ttdoc">Compute the diffusion relaxation process of all species with second order Runge-Kutta time stepping.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:186</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html_a7e1a1c79e4b69348aea7e9644fe1de57"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#a7e1a1c79e4b69348aea7e9644fe1de57">SPH::RelaxationOfAllDiffusionSpeciesRK2::species_s_</a></div><div class="ttdeci">StdVec&lt; StdLargeVec&lt; Real &gt; &gt; species_s_</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:192</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_relaxation_of_all_diffussion_species_inner_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffussion_species_inner.html">SPH::RelaxationOfAllDiffussionSpeciesInner</a></div><div class="ttdoc">Compute the diffusion relaxation process of all species.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:97</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_get_diffusion_time_step_size_html"><div class="ttname"><a href="class_s_p_h_1_1_get_diffusion_time_step_size.html">SPH::GetDiffusionTimeStepSize</a></div><div class="ttdoc">Computing the time step size based on diffusion coefficient and particle smoothing length.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:78</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_initial_condition_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">SPH::DiffusionReactionInitialCondition</a></div><div class="ttdoc">pure abstract class for initial conditions</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:61</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_particle_dynamics_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics.html">SPH::ParticleDynamics</a></div><div class="ttdoc">The base class for all particle dynamics This class contains the only two interface functions availab...</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:122</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_runge_kutta_initialization_html"><div class="ttname"><a href="class_s_p_h_1_1_runge_kutta_initialization.html">SPH::RungeKuttaInitialization</a></div><div class="ttdoc">initialization of a runge-kutta integration scheme</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:147</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_base_inner_body_relation_html"><div class="ttname"><a href="class_s_p_h_1_1_base_inner_body_relation.html">SPH::BaseInnerBodyRelation</a></div><div class="ttdoc">The base relation within a SPH body.</div><div class="ttdef"><b>Definition:</b> body_relation.h:110</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_base_reaction_model_html"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html">SPH::BaseReactionModel</a></div><div class="ttdoc">Base class for all reaction models.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:154</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_part_simple_dynamics_by_particle_html"><div class="ttname"><a href="class_s_p_h_1_1_part_simple_dynamics_by_particle.html">SPH::PartSimpleDynamicsByParticle</a></div><div class="ttdoc">Abstract class for body part simple particle dynamics.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_bodypart.h:63</div></div>
<div class="ttc" id="astruct_s_p_h_1_1_update_a_reaction_species_html"><div class="ttname"><a href="struct_s_p_h_1_1_update_a_reaction_species.html">SPH::UpdateAReactionSpecies</a></div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:206</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_interaction_dynamics_with_update_html"><div class="ttname"><a href="class_s_p_h_1_1_interaction_dynamics_with_update.html">SPH::InteractionDynamicsWithUpdate</a></div><div class="ttdoc">This class includes an interaction and a update steps.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:155</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_get_diffusion_time_step_size_html_abbafdb225bf35578cb3d8d891f54b1e9"><div class="ttname"><a href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">SPH::GetDiffusionTimeStepSize::exec</a></div><div class="ttdeci">virtual Real exec(Real dt=0.0) override</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:86</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_constrain_diffusion_body_region_html"><div class="ttname"><a href="class_s_p_h_1_1_constrain_diffusion_body_region.html">SPH::ConstrainDiffusionBodyRegion</a></div><div class="ttdoc">set boundary condition for diffusion problem</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:257</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_data_delegate_inner_html"><div class="ttname"><a href="class_s_p_h_1_1_data_delegate_inner.html">SPH::DataDelegateInner</a></div><div class="ttdoc">prepare data for inner particle dynamics</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:190</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_s_p_h_body_html"><div class="ttname"><a href="class_s_p_h_1_1_s_p_h_body.html">SPH::SPHBody</a></div><div class="ttdoc">SPHBody is a base body with basic data and functions. Its derived class can be a real fluid body,...</div><div class="ttdef"><b>Definition:</b> base_body.h:63</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_particle_dynamics_simple_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics_simple.html">SPH::ParticleDynamicsSimple</a></div><div class="ttdoc">Simple particle dynamics without considering particle interaction.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:46</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_based_mapping_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_based_mapping.html">SPH::DiffusionBasedMapping</a></div><div class="ttdoc">Mapping inside of body according to diffusion. This is a abstract class to be override for case speci...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:278</div></div>
<div class="ttc" id="aclass_real_html"><div class="ttname"><a href="class_real.html">Real</a></div></div>
<div class="ttc" id="anamespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> solid_body_supplementary.cpp:9</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_relaxation_of_all_reactions_forward_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">SPH::RelaxationOfAllReactionsForward</a></div><div class="ttdoc">Compute the reaction process of all species by forward splitting.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:219</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_data_delegate_simple_html"><div class="ttname"><a href="class_s_p_h_1_1_data_delegate_simple.html">SPH::DataDelegateSimple</a></div><div class="ttdoc">prepare data for simple particle dynamics.</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:164</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_relaxation_of_all_reactions_backward_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">SPH::RelaxationOfAllReactionsBackward</a></div><div class="ttdoc">Compute the reaction process of all species by backward splitting.</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:238</div></div>
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.17
</small></address>
</body>
</html>
